The page is a central reference of information and notes for computational biologists and software engineers in the CGA group, as we transition from the TCGA era of GDAC to the GDC/GDAN era. As of July 2016, the Genomics Data Commons has replaced the TCGA Data Coordination Center as the repository of not only TCGA data but also for other existing genomics projects (such as TARGET), as well as future genomics projects.

Reference Data

For GDAN pipelines we will store on-premises reference data in /xchip/cga/reference/GDAN.

This is analogous to the TCGA reference directory /xchip/cga/reference/tcga but is not TCGA-centric. In addition to having hg38 reference data, the GDAN reference tree will gather the bits and pieces of "hidden data" that for expedience has been accidentally squirreled away in less than ideal locations.